fmriprep

a BIDS app that runs a standardized and reproducible preprocessing pipeline on structural and functional MRI data

Running fmriprep

Oscar

1. Write a batch script

We keep up-to-date Singularity images for fmriprep for the community. (Look in /oscar/data/bnc/simgs/nipreps/ to see which versions we currently have available.) In order to run fmriprep on Oscar, you'll need to write a batch script. Here is an example:

demodat_fmriprep_example.sh -- Filename and not part of the script!

#!/bin/bash
#SBATCH -N 1
#SBATCH -c 8
#SBATCH --mem=32G
#SBATCH --time 18:00:00
#SBATCH -J fmriprep
#SBATCH --output fmriprep-log-%J.txt
#SBATCH --mail-user [email protected]
#SBATCH --mail-type ALL

#---------CONFIGURE THESE VARIABLES--------------
export_dir=/oscar/data/<group>/<user>/xnat-exports/bnc/study-demodat
participant_label=005
fmriprep_version=24.1.0
#---------END OF VARIABLES------------------------

singularity run --cleanenv                                         \
  --bind ${export_dir}:/data                    \
  --bind /oscar/scratch/${USER}:/scratch                            \
  --bind /oscar/data/bnc/licenses:/licenses                         \
  /oscar/data/bnc/simgs/nipreps/fmriprep-${fmriprep_version}.sif    \
  /data/bids /data/bids/derivatives/fmriprep-${fmriprep_version}   \
  participant --participant-label ${participant_label}             \
  --output-spaces T1w MNI152NLin2009cAsym MNI152NLin6Asym:res-2    \
  --fs-license-file /licenses/freesurfer-license.txt               \
  -w /scratch/fmriprep                                             \
  --omp-nthreads 16 --nthreads 16 --stop-on-first-crash

✋Understanding the batch script

• The first part of the script configures the variables (e.g., number of cores, memory, etc) for your JOB. Make sure to update the email address if you'd like to get email updates about your job.

• The second part invokes fmriprep singularity image. Keep in mind the following considerations:

  • Singularity containers run as your user, and therefore should have the same read/write permissions as your local user in the cluster

  • Singularity containers only share $HOME with the Oscar file system. Therefore, any other location that we want to read and write to/from, needs to be specified using the --bind hostfolder:containerfolder input. This includes any directory in your home directory that is a symbolic link. For instance $HOME/data usually points to /oscar/data/<group> in that case we must bind /oscar/data/<group>

  • You must specify the location inside the container of the FreeSurfer license.

2. Run the batch script

cd /path/to/sbatch/script
sbatch demodat_fmriprep_example.sh

For more information about managing your job, see the Oscar documentation

✋ Troubleshooting:

fmriprep may fail for many reasons. Here are few tips:

• Freesurfer is often difficult to get to completion, if it helps troubleshooting, you can turn FreeSurfer reconstruction off by adding the flag --fs-no-reconall

• Familiarize yourself with the inputs and don't hesitate to ask the developers questions. Good places to look/ask for help are their GitHub issues and the Neurostars forum

⚠️ At least as of fmriprep version 23.1.3, susceptibility distortion correction performs very poorly if you supply phase difference field maps like we have in the demodat dataset, actually making distortion worse. Distortion correction performance is much better with the 20.2.7 LTS version of fmriprep, which we also have available on Oscar.

Docker

Getting a different version than what is installed in Oscar.

If you wish to use a version not available under /oscar/data/bnc/simg/nipreps, you'll need to build the image. Singularity images can be large, therefore consider using a place with sufficient quota and changing the default location singularity uses to cache these files. Please see Oscar documentation.

To build the image, you can run:

version=22.0.0
singularity build fmriprep-${version}.sif docker://nipreps/fmriprep:${version}

Replace version in the command above with the desired docker tag. You can find the latest tags of fmriprep here

To support scientific reproducibility, it is recommended to use a specific tag e.g., 22.0.0 instead of latest